#Lines starting with hash (#) are ignored
#Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder
clustalOmegaCommand=clustalo
hmmbuildCommand=hmmbuild
hmmsearchCommand=hmmsearch
hhmakeCommand=hhmake
hhsearchCommand=hhsearch
#Directory for all temporal files. Define full path if needed. Default (not specified): /tmp
#tempDirectory=
#Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/
#fastaDirectory=
#msaDirectory=
#hmmDirectory=
#hhDirectory=
#hmmsearchOutDirectory=
#hhsearchOutDirectory=
#fastaDatabaseFile=
#Tool parameters. Generally, it is not recommended to change this section.
clustalOmegaParameters=--wrap=999999
hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42
hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --notextw -E 999999 --seed 42
hmmalignParameters=--outformat selex --amino --seed 42
hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0
hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100
